Welcome to karyoplot documentation!

Author

Rosanne Phebe, Nicolas Lapalu and Adeline Simon - BioinfoBioger team

Date

Jul 11, 2022

Version

0.0.2

What is karyoplot ?

karyoplot is a python package developed to draw simple karyoplot/ideogram with a simple coniguration file like Circos 1, without any lines of code like karyoploteR 2. The goal of karyoplot is use to deal with conventional bioinformatics formats (.bed, .fasta, .gff, .gtf, .vcf, …) to avoid file manipulations before drawing.

How does it work ?

karyoplot takes as an argument a configuration file with different sections which will have a sequence Fasta file as reference for ideograms. Every plot to draw on reference sequences is described in a track section with link to associated data and drawing options. karyoplot is mainly based on matplotlib for graph rendering and pysam for bioinformatics file format parsing.

To start off, a well-formatted configuration file is required, you can learn how to set yours options. The config.ini file is a configuration file in Microsoft Windows INI style, readable by the configparser Python module.

karyoplot is under developpement, currently supported format are:

• fasta

• bed

available soon:

• gff

• vcf

• bam

• wig/bigWig

License

licensed under GNU General Public License v3.0

Support

For any request please contact nicolas.lapalu[at]inrae.fr or adeline.simon[at]inrae.fr

References

1

Krzywinski, M. et al. Circos: an Information Aesthetic for Comparative Genomics. Genome Res (2009) 19:1639-1645

2

Bernat Gel & Eduard Serra. (2017). karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics, 31–33. doi:10.1093/bioinformatics/btx346